6dxv - Revision history

OCA at 06:15, 11 October 2023

2023-10-11T06:15:33Z

←Older revision		Revision as of 06:15, 11 October 2023
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	==Citrobacter freundii tyrosine phenol-lyase F448A mutant==		==Citrobacter freundii tyrosine phenol-lyase F448A mutant==
-	<StructureSection load='6dxv' size='340' side='right' caption='[[6dxv]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='6dxv' size='340' side='right'caption='[[6dxv]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dxv]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacterium_freundii"_braak_1928 "bacterium~~ freundii~~" braak 1928~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DXV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DXV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dxv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Citrobacter_freundii Citrobacter freundii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DXV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DXV FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=K:POTASSIUM+ION'>K</scene~~></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.2Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene~~></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tpl ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=546 "Bacterium freundii" Braak 1928])</td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6dxv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dxv OCA], [https://pdbe.org/6dxv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dxv RCSB], [https://www.ebi.ac.uk/pdbsum/6dxv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dxv ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tyrosine_phenol-lyase Tyrosine phenol-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.99.2 4.1.99.2] </span></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6dxv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dxv OCA], [~~http~~://pdbe.org/6dxv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dxv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dxv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dxv ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/TPL_CITFR TPL_CITFR]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6dxv" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6dxv" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Tyrosinase 3D structures\|Tyrosinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacterium~~ freundii ~~braak 1928~~]]	+	[[Category: Citrobacter freundii]]
-	[[Category: ~~Tyrosine phenol-lyase~~]]	+	[[Category: Large Structures]]
-	[[Category: Phillips~~, R S]]~~	+	[[Category: Phillips RS]]
-	~~[[Category: Aminotransferase fold]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Pyridoxal-5'-phosphate~~]]	+

OCA at 08:58, 14 November 2018

2018-11-14T08:58:55Z

←Older revision		Revision as of 08:58, 14 November 2018
Line 3:		Line 3:
	<StructureSection load='6dxv' size='340' side='right' caption='[[6dxv]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6dxv' size='340' side='right' caption='[[6dxv]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dxv]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DXV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DXV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dxv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_freundii"_braak_1928 "bacterium freundii" braak 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DXV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DXV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tpl ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=546 "Bacterium freundii" Braak 1928])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tyrosine_phenol-lyase Tyrosine phenol-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.99.2 4.1.99.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tyrosine_phenol-lyase Tyrosine phenol-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.99.2 4.1.99.2] </span></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6dxv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dxv OCA], [http://pdbe.org/6dxv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dxv RCSB], [http://www.ebi.ac.uk/pdbsum/6dxv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dxv ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6dxv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dxv OCA], [http://pdbe.org/6dxv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dxv RCSB], [http://www.ebi.ac.uk/pdbsum/6dxv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dxv ProSAT]</span></td></tr>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacterium freundii braak 1928]]
	[[Category: Tyrosine phenol-lyase]]		[[Category: Tyrosine phenol-lyase]]
	[[Category: Phillips, R S]]		[[Category: Phillips, R S]]

OCA at 08:07, 10 October 2018

2018-10-10T08:07:24Z

←Older revision		Revision as of 08:07, 10 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6dxv is ~~ON HOLD until Paper~~ Publication	+	==Citrobacter freundii tyrosine phenol-lyase F448A mutant==
		+	<StructureSection load='6dxv' size='340' side='right' caption='[[6dxv]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6dxv]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DXV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DXV FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tyrosine_phenol-lyase Tyrosine phenol-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.99.2 4.1.99.2] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6dxv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dxv OCA], [http://pdbe.org/6dxv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dxv RCSB], [http://www.ebi.ac.uk/pdbsum/6dxv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dxv ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Tyrosine phenol-lyase (TPL; E.C. 4.1.99.2) is a pyridoxal-5'-phosphate dependent enzyme that catalyzes the reversible hydrolytic cleavage of L-tyrosine to phenol and ammonium pyruvate. We have shown previously that F448A TPL has kcat and kcat/Km values for L-tyrosine reduced by about 104 (Phillips, R. S., Vita, A., Spivey, J. B., Rudloff, A. P., Driscoll, M. D., & Hay, S. (2016) ACS Catalysis, 6, 6770-6779). We have now obtained crystal structures of F448A TPL and complexes with L-alanine, L-methionine, L-phenylalanine, and 3-F-L-tyrosine at 2.05-2.27 A, as well as the complex of wild-type TPL with L-phenylalanine at 1.8 A. The small domain of F448A TPL, where Phe-448 is located, is more disordered in chain A than wild-type TPL. The complexes of F448A TPL with L-alanine and L-phenylalanine are in an open conformation in both chains, while the complex with L-methionine is a 52:48 equilibrium mixture of open and closed conformations, respectively, in chain A. Wild-type TPL with L-alanine is closed in chain A and open in chain B, and the complex with L-phenylalanine is 56:44 in open and closed conformations in chain A. Thus, the Phe-448 to alanine mutation affects the conformational equilibrium of open and closed active sites. The structure of the 3-F-L-tyrosine quinonoid complex of F448A TPL is unstrained and in an open conformation, with a hydrogen bond from the phenolic OH to Thr-124. These results support our previous conclusion that ground-state strain plays a critical role in the mechanism of TPL.

-	~~Authors~~: Phillips, R.S.	+	Crystal Structures of Wild-type and F448A Mutant Citrobacter freundii Tyrosine Phenol-lyase Complexed with Substrate and Inhibitors: Implications for the Reaction Mechanism.,Phillips RS, Craig S Biochemistry. 2018 Sep 27. doi: 10.1021/acs.biochem.8b00724. PMID:30260636<ref>PMID:30260636</ref>

-	~~Description: Citrobacter freundii tyrosine phenol~~-~~lyase F448A mutant~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Phillips, R.S]]	+	<div class="pdbe-citations 6dxv" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Tyrosine phenol-lyase]]
		+	[[Category: Phillips, R S]]
		+	[[Category: Aminotransferase fold]]
		+	[[Category: Lyase]]
		+	[[Category: Pyridoxal-5'-phosphate]]

OCA at 08:40, 5 September 2018

2018-09-05T08:40:43Z

←Older revision		Revision as of 08:40, 5 September 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6dxv is ON HOLD	+	The entry 6dxv is ON HOLD until Paper Publication

	Authors: Phillips, R.S.		Authors: Phillips, R.S.

OCA: Protected "6dxv" [edit=sysop:move=sysop]

2018-07-11T04:06:18Z

Protected "6dxv" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:06, 11 July 2018

OCA: New page: '''Unreleased structure''' The entry 6dxv is ON HOLD Authors: Phillips, R.S. Description: Citrobacter freundii tyrosine phenol-lyase F448A mutant Category: Unreleased Structures [[...

2018-07-11T04:06:17Z

New page: '''Unreleased structure''' The entry 6dxv is ON HOLD Authors: Phillips, R.S. Description: Citrobacter freundii tyrosine phenol-lyase F448A mutant Category: Unreleased Structures [[...

New page

'''Unreleased structure'''

The entry 6dxv is ON HOLD

Authors: Phillips, R.S.

Description: Citrobacter freundii tyrosine phenol-lyase F448A mutant
[[Category: Unreleased Structures]]
[[Category: Phillips, R.S]]